Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here we present a systematic analysis of fifteen RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt A-form RNA in the stem region. Loop structures are more sensitive and experimental structures could only be reproduced with modification of CH---O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future.